The mobilome is the total of all mobile genetic elements in a genome. Elements that can move within the genome (transposable elements) are the major constitients of the mobilome in eukaryotes. In prokaryotes, however, mobile genetic elements that can move between genomes, like prophages and plasmids, are also an important part of the mobilome.
References
Barkay, T. and Smets, B.F. 2005. Horizontal gene flow in microbial communities. ASM News 71: 412-419.
Frost, L.S. et al., 2005. Mobile genetic elements: the agents of open source evolution. Nat. Rev. of Microbiology 3: 722-732.
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